Getting started

Gel Report Models is now available both in Python 2 and Python 3. Depending on your version of python and pip when you install it, it will install the appropriate version for your environment.

0. Clone this repository:

git clone git@github.com:genomicsengland/ACGS_GeL_API_workshop.git

or

git clone https://github.com/genomicsengland/ACGS_GeL_API_workshop.git

if using https.

1. Change into the directory:

cd ACGS_GeL_API_workshop

2. Install virtualenv if you don't have it already or upgrade if you do:

pip install --upgrade virtualenv

3. Then create a virtual environment and install the requirements:

virtualenv .env
source ./.env/bin/activate
pip install -r requirements.txt

4. Either place your CIP API credentials and the url of the server you want to use in the notebook, or create a file (e.g. cip_api_credentials):

export CIP_API_USERNAME="username"
export CIP_API_PASSWORD="password"
export CIP_API_SERVER_URL="https://cipapi-server-url/api/{endpoint}"

adding your credentials and the server you want to conect to.

5. Then run:

source cip_api_credentials

6. -Optional- to use Gel-Models

git clone git@github.com:genomicsengland/GelReportModels.git
cd GelReportModels
pip install .

7. You should now be able to run the notebook:

jupyter-notebook CIP_API_examples.ipynb

This will open the notebook in http://localhost:8888/notebooks/CIP_API_examples.ipynb

GelReportModels Doc https://genomicsengland.github.io/GelReportModels/